Phenotypic Description of Theobroma cacao L. for Yield and Vigor Traits From 34 Hybrid Families in Costa Rica Based on the Genetic Basis of the Parental Population.

A comprehensive understanding of the genetic basis of target traits in any crop is critical to design breeding strategies for the development and release of new improved varieties. In this study, 34 cacao families were evaluated for vigor and yield related traits over the course of 6 years in Costa Rica. Linear mixed models provided the variance components for the partitioning of additive and non-additive effects. Heritabilities of yield over time ranged from 0.085 to 0.576, from 0.127 to 0.399 for vigor, and 0.141 to 0.146 for disease resistance traits. Significant (p < 0.001) general combining abilities were observed for ICS-43 and LcTeen-37 with negative effect on average yield (-0.674, -0.690), respectively. Specific combining abilities for yield had significant (p < 0.001) positive effect from the cross GU-154-L x UF-273 Type 2 (0.703) and strong negative interaction between ICS-43 and LF-1 (-0.975). A weighted index was used to select the top performers while providing the corresponding genetic gains. At an 1% selection intensity, yield component gains ranged from 17.8 to 331.9%. Agronomic traits such as branch angle, trunk diameter and jorquette height had lower genetic gains and lower heritabilities. In addition, the parents in this study were genotyped with a 96-SNP marker off-typing set and a significant positive correlation of 0.39 (p = 0.019) was found between genetic distance and specific combining abilities for yield. Preliminary comparison of clonal parents vs. seedlings yield in the family with the highest SCA suggest for the first time presence of heterobeltiosis in cacao.

Moniliophthora roreri, causal agent of cacao frosty pod rot.

Taxonomy: Moniliophthora roreri (Cif.) H.C. Evans et al. ; Phylum Basidiomycota; Class Agaricomycetes; Order Agaricales; Family Marasmiaceae; Genus Moniliophthora. Biology: Moniliophthora roreri attacks Theobroma and Herrania species causing frosty pod rot. Theobroma cacao (cacao) is the host of major economic concern. Moniliophthora roreri is a hemibiotroph with a long biotrophic phase (45-90 days). Spore masses, of apparent asexual origin, are produced on the pod surface after initiation of the necrotrophic phase. Spores are spread by wind, rain and human activity. Symptoms of the biotrophic phase can include necrotic flecks and, in some cases, pod malformation, but pods otherwise remain asymptomatic. Relationship to Moniliophthora perniciosa: Moniliophthora roreri and Moniliophthora perniciosa, causal agent of witches' broom disease of cacao, are closely related. Their genomes are similar, including many of the genes they carry which are considered to be important in the disease process. Moniliophthora perniciosa, also a hemibiotroph, has a typical basidiomycete lifestyle and morphology, forming clamp connections and producing mushrooms. Basidiospores infect meristematic tissues including flower cushions, stem tips and pods. Moniliophthora roreri does not form clamp connections or mushrooms and infects pods only. Both pathogens are limited to the Western Hemisphere and are a threat to cacao production around the world. Agronomic importance: Disease losses caused by frosty pod rot can reach 90% and result in field abandonment. Moniliophthora roreri remains in the invasive phase in the Western Hemisphere, not having reached Brazil, some islands within the Caribbean and a few specific regions within otherwise invaded countries. DISEASE MANAGEMENT: The disease can be managed by a combination of cultural (for example, maintenance of tree height and removal of infected pods) and chemical methods. These methods benefit from regional application, but can be cost prohibitive. Breeding for disease resistance offers the greatest potential for frosty pod rot management and new tolerant materials are becoming available.

Assessing hidden parentage and genetic integrity of the "United Fruit Clones" of cacao (Theobroma cacao) from Costa Rica using SNP markers.

The international cacao collection in CATIE, Costa Rica contains nearly 1200 accessions of cacao, mainly from the center of genetic diversity of this species. Among these accessions, the United Fruit clones (UF clones) were developed by the United Fruit Company in Costa Rica, and they represent one of the earliest groups of improved cacao germplasm in the world. Some of these UF clones have been used as key progenitors for breeding resistance/tolerance to Frosty Pod and Black Pod diseases in the Americas. Accurate information on the identity and background of these clones is important for their effective use in breeding. Using Single Nucleotide Polymorphism (SNP) markers, we genotyped 273 cacao germplasm accessions including 44 UF clones and 229 reference accessions. We verified the true-to-type identity of UF clones in the CATIE cacao collection and analyzed their population memberships using maximum-likelihood-based approaches. Three duplicate groups, representing approximately 30% of the UF clones, were identified. Both distance- and model-based clustering methods showed that the UF clones were mainly composed of Trinitario, ancient Nacional and hybrids between ancient Nacional and Amelonado. This result filled the information gap about the UF clones thus will improve their utilization for cacao breeding.

Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases.

Chocolate is a highly valued and palatable confectionery product. Chocolate is primarily made from the processed seeds of the tree species Theobroma cacao. Cacao cultivation is highly relevant for small-holder farmers throughout the tropics, yet its productivity remains limited by low yields and widespread pathogens. A panel of 148 improved cacao clones was assembled based on productivity and disease resistance, and phenotypic single-tree replicated clonal evaluation was performed for 8 years. Using high-density markers, the diversity of clones was expressed relative to 10 known ancestral cacao populations, and significant effects of ancestry were observed in productivity and disease resistance. Genome-wide association (GWA) was performed, and six markers were significantly associated with frosty pod disease resistance. In addition, genomic selection was performed, and consistent with the observed extensive linkage disequilibrium, high predictive ability was observed at low marker densities for all traits. Finally, quantitative trait locus mapping and differential expression analysis of two cultivars with contrasting disease phenotypes were performed to identify genes underlying frosty pod disease resistance, identifying a significant quantitative trait locus and 35 differentially expressed genes using two independent differential expression analyses. These results indicate that in breeding populations of heterozygous and recently admixed individuals, mapping approaches can be used for low complexity traits like pod color cacao, or in other species single gene disease resistance, however genomic selection for quantitative traits remains highly effective relative to mapping. Our results can help guide the breeding process for sustainable improved cacao productivity.

Effects of microclimatic variables on the symptoms and signs onset of Moniliophthora roreri, causal agent of Moniliophthora pod rot in cacao.

Moniliophthora Pod Rot (MPR) caused by the fungus Moniliophthora roreri (Cif.) Evans et al., is one of the main limiting factors of cocoa production in Latin America. Currently insufficient information on the biology and epidemiology of the pathogen limits the development of efficient management options to control MPR. This research aims to elucidate MPR development through the following daily microclimatic variables: minimum and maximum temperatures, wetness frequency, average temperature and relative humidity in the highly susceptible cacao clone Pound-7 (incidence = 86% 2008-2013 average). A total of 55 cohorts totaling 2,268 pods of 3-10 cm length, one to two months of age, were tagged weekly. Pods were assessed throughout their lifetime, every one or two weeks, and classified in 3 different categories: healthy, diseased with no sporulation, diseased with sporulating lesions. As a first step, we used Generalized Linear Mixed Models (GLMM) to determine with no a priori the period (when and for how long) each climatic variable was better related with the appearance of symptoms and sporulation. Then the significance of the candidate variables was tested in a complete GLMM. Daily average wetness frequency from day 14 to day 1, before tagging, and daily average maximum temperature from day 4 to day 21, after tagging, were the most explanatory variables of the symptoms appearance. The former was positively linked with the symptoms appearance when the latter exhibited a maximum at 30°C. The most important variables influencing sporulation were daily average minimum temperature from day 35 to day 58 and daily average maximum temperature from day 37 to day 48, both after tagging. Minimum temperature was negatively linked with the sporulation while maximum temperature was positively linked. Results indicated that the fungal microclimatic requirements vary from the early to the late cycle stages, possibly due to the pathogen's long latent period. This information is valuable for development of new conceptual models for MPR and improvement of control methods.